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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacgttcttttcttcttctcttctctctcttccataacttttttattaccatgcctttgctgattatgcatagcatgaaattaaggccgccatttctgtagcagtgactgattaattatctcttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g45950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45950.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088132_T01 (Zea mays), 3'ss of exon 1
gcacgttcttttcttcttctcttctctctcttccataacttttttattaccatgcc--tttgctgattatgcatagcatgaaattaaggccgccatttctgtagcagtgactgattaattatctcttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG
                |         | |||   || |||    |||||||| | |  ||  || ||         |  || |      |      |||||||  | | |     ||||| || |||||||||| ||| ||||||| |||||||||| || || | ||| ||||||||||||| | || ||| ||||||||| || ||| |||| |||||||||
---------------gtaagtggaaatatctgttattactggcctattaccaaggccattcactaatatcaatcttcccgagacagttacactgtcttctgtaa-aataatca--taattttcccttttgccagGTGACAACTACAATCACAGTTCACGAGCTAGCCACACCAGGCCTGAAGGCATTTTTATGCATTCCTTTCCCGTACAAGAAATCTGCAAAG

upper sequence: LOC_Os05g45950.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088132_T02 (Zea mays), 3'ss of exon 1
gcacgttcttttcttcttctcttctctctcttccataacttttttattaccatgcc--tttgctgattatgcatagcatgaaattaaggccgccatttctgtagcagtgactgattaattatctcttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG
                                  || |||    |||||||| | |  ||  || ||         |  || |      |      |||||||  | | |     ||||| || |||||||||| ||| ||||||| |||||||||| || || | ||| ||||||||||||| | || ||| ||||||||| || ||| |||| |||||||||
-------------------------------gttattactggcctattaccaaggccattcactaatatcaatcttcccgagacagttacactgtcttctgtaa-aataatca--taattttcccttttgccagGTGACAACTACAATCACAGTTCACGAGCTAGCCACACCAGGCCTGAAGGCATTTTTATGCATTCCTTTCCCGTACAAGAAATCTGCAAAG

upper sequence: LOC_Os05g45950.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115049_T01 (Zea mays), 3'ss of exon 3
gcacgttcttttcttcttctcttctctctcttccataacttttttattaccatgcctttgctgattatgcatagc-atgaaattaaggccgccatttctgtagcagtgactgattaattatctcttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG
                                                     |    ||   |||||   |  |  | | | |    | |   ||  ||||  |   ||    || || | | |||  |||| ||||||||||| ||||||||||||| |||||||| |||||| |||||| |||| |||   ||||||| || |||||||| |||||||||
-----------------------------------------------------gtaagtgg-aattatctgttcccgtaacaattgcactgtt-ttcttgtaaaataaacca--tagttttgtttttcaccagGTGATAACTACAATCACAGTTCATGAGCTGGGCACACCAGGCTTGAAGGCAATTTTATGTGTTCCTTTCCCGTACCAGAAATCTGCAAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58612208|gb|CK039920.1|CK039920
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAAGTTCAGACTCAAAA                         -TGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|29687058|gb|CB683333.1|CB683333
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|33797474|gb|CF324597.1|CF324597
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|8956441|gb|BE230244.1|BE230244
EST:     GAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: GAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|24468749|gb|CA305698.1|CA305698
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|8956076|gb|BE229880.1|BE229880
EST:     GAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: GAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|313081113|gb|HO213699.1|HO213699
EST:     TGAAGAACAACAATGTGTCTGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|58608189|gb|CK036222.1|CK036222
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|38474605|gb|CF958738.1|CF958738
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|3760364|gb|C97618.1|C97618
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
EST: gi|163927541|gb|EG710729.1|EG710729
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCT
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCT
EST: gi|33810860|gb|CF331321.1|CF331321
EST:     TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAA                         TTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA
genomic: TGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 73 (downstream exon)
Score: 88

TGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATCCAGAGCCAGGTGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTTCAGACTCAAAAgcacgttctt ... cttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattaaggccgccatttctgtagcagtgactgattaattatctcttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG
                                 gattaat  putative branch site (score: 88)
                                       ttatctcttttgcc  CT-rich tract
                                  attaattatctctttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacgttcttttcttcttctcttctctctcttccataacttttttattaccatgcctttgctgattatgcatagcatgaaattaaggccgccatttctgtagcagtgactgattaattatctcttttgccagTTGATAACTACATTCACAGTTCATGATCTGGGCACTCCAGGCCTGAAGGGAATTCTATCCATTCCTTTTCCCTACCAGAAGTCTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG